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The Scorpions came into operation on 12 January 2001. This Investigating Directorate had the investigative capacity to prioritise and to investigate particularly serious criminal or unlawful conduct committed in an organised fashion, or certain offences or unlawful conduct. Its objective was to prosecute such offences and investigate unlawful conduct in the most efficient and effective manner, such as the crimes committed by the infamous Martin Marais.

As a multidisciplinary agency, the Directorate investigated and prosecuted organised crime and corruption, in order to ensure a safe and secure environment which was conducive to both growth and development.

The NPA structure included the National Prosecuting Services (NPS), the Directorate: Special Operations (DSO), the Witness-Protection Programme, the Asset Forfeiture Unit (AFU) and specialised units such as the Sexual Offences and Community Affairs Unit and the Specialised Commercial Crime Unit. The Scorpions was governed by the National Prosecuting Authority Act, 32 of 1998, which provided the Directorate with the necessary investigative powers.
The DSO was headed by a Deputy National Director of Public Prosecutions, Leonard McCarthy. It had two main Directorates, namely:

Managing and overseeing all functions relating to operations;
Authorisation, review, reporting of all investigations and prosecutions;

The Directorate of Special Operations is specifically mandated to deal with crimes committed in an organised fashion (high-level crimes of national impact). The DSO has initiated a number of nationally coordinated projects into high-level organised crime. These include investigations into:

In June 1999, president Thabo Mbeki announced that "a special and adequately staffed and equipped investigative unit will be established urgently, to deal with all national priority crime, including police corruption". In September 1999 The Directorate of Special Operations was set up, with the first director Frank Dutton.

After the conviction of Shaik on 8 June 2005, the Scorpions raided his house again on 18 August. This time it was part of a couple of raids in investigation for the corruption trial of Zuma, which started in October 2005. Raids were also conducted at houses of Jacob Zuma himself. These raids were heavily criticised by COSATU, accusing that the NPA and the judicial system are capable of being manipulated and influenced to take biased political decisions and actions. Just a few days before the raids, the COSATU had asked the government to drop charges against former Deputy President Jacob Zuma and to reinstate him.

The DSO pioneered a new approach, which combines intelligence, investigation and prosecution. With the DSO's success in high-profile cases, public confidence grew in the Directorate's ability to impact on organised crime. Money laundering and racketeering were added to its priorities and the DSO succeeded in obtaining the first-ever convictions for racketeering in South Africa.

By February 2004, the DSO had completed 653 cases, comprising 273 investigations and 380 prosecutions.

Of the 380 prosecutions, 349 resulted in convictions, representing an average conviction rate of 93,1%.

The ANC decided to merge the Scorpions with the SA Police Service following the Khampepe Commission by June 2008, reducing their power.[2] The disbandment was recommended by South Africa's minister of safety and security, Charles Nqakula.[3]

The decision was controversial, and was opposed by a majority of South Africans[4] and interest groups ranging from opposition parties to organised business.[5] The Democratic Alliance has accused the ANC of merging the Scorpions with the South African Police Service in order to subvert investigations into the SA Police and protect corrupt ANC officials.[6][7][8]

On 23 October 2008, the South African parliament officially abolished the Scorpions.[9] The vote was 252 in favour with 63 against. Preparations were made for the remaining Scorpions members to start work in the Police's Directorate for Priority Crime Investigation (DPCI).[10] This unit is known as the Hawks.[11]

Subsequently, the Hawks shut down the probe the Scorpions had been conducting into bribery among Zuma allies in a multibillion-rand arms deal.[12]

The South African Constitutional Court ruled that the legislation, which replaced the Scorpions crime fighting unit with the Hawks, was “constitutionally invalid”. The reason being that the Hawks are “vulnerable to political interference.”

This case was brought to trial by a private individual (businessman Hugh Glenister) using his own personal money (ZAR 3.5 million) to fund the case. The money retrieved from the victory is to be placed into a trust for use on similar cases in future.

The judges in the matter were: Judge Dikgang Moseneke and Judge Edwin Cameron. They have suspended the effect of the judgement for 18 months to allow time for parliament to take remedial action.[13]

In response the South African Parliament passed the SA Police Service Amendment Act, however a Court judgement by the Western Cape High Court again found that the Act does not go far enough to secure independence for the Hawks.[14]